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Bdellovibrio bacteriovorus PGI in complex with fructose-6-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 0.2 M ammonium acetate
0.1 M sodium acetate pH 5.0
20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.2 α = 90 b = 101.2 β = 90 c = 76.38 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.67 43.82 99.9 0.057 0.06 0.019 1 25 19.6 52651 41.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 99.9 1.966 2.073 0.655 0.822 1.5 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7NSS 1.67 43.82 50006 2616 97.02 0.1799 0.1781 0.2167 0.2199 RANDOM 36.123
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.85 0.43 0.85 -2.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.564 r_dihedral_angle_4_deg 19.793 r_dihedral_angle_3_deg 13.734 r_dihedral_angle_1_deg 6.62 r_angle_other_deg 2.293 r_angle_refined_deg 1.63 r_chiral_restr 0.089 r_bond_other_d 0.034 r_gen_planes_other 0.013 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.564 r_dihedral_angle_4_deg 19.793 r_dihedral_angle_3_deg 13.734 r_dihedral_angle_1_deg 6.62 r_angle_other_deg 2.293 r_angle_refined_deg 1.63 r_chiral_restr 0.089 r_bond_other_d 0.034 r_gen_planes_other 0.013 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3163 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction